\docType{methods}
\name{get.methylDiff}
\alias{get.methylDiff}
\alias{get.methylDiff,methylDiff-method}
\title{get differentially methylated regions/bases based on cutoffs}
\usage{
  get.methylDiff(.Object,difference=25,qvalue=0.01,type="all")
}
\arguments{
  \item{.Object}{a \code{\link{methylDiff}} object}

  \item{difference}{cutoff for absolute value of %
  methylation change between test and control (default:25)}

  \item{qvalue}{cutoff for qvalue of differential
  methylation statistic (default:0.01)}

  \item{type}{one of the "hyper","hypo" or "all" strings.
  Specifies what type of differentially menthylated
  bases/regions should be returned.  For retrieving
  Hyper-methylated regions/bases type="hyper", for
  hypo-methylated type="hypo" (default:"all")}
}
\value{
  a methylDiff object containing the differential
  methylated locations satisfying the criteria
}
\description{
  The function subsets a \code{\link{methylDiff}} object in
  order to get differentially methylated bases/regions
  satisfying thresholds.
}
\examples{
data(methylKit)

# get differentially methylated bases/regions with specific cutoffs
all.diff=get.methylDiff(methylDiff.obj,difference=25,qvalue=0.01,type="all")

# get hyper-methylated
hyper=get.methylDiff(methylDiff.obj,difference=25,qvalue=0.01,type="hyper")

# get hypo-methylated
hypo=get.methylDiff(methylDiff.obj,difference=25,qvalue=0.01,type="hypo")
}

